Seohyun Lee - The University of Tokyo

Education

Oct. 2014.	-	Sep. 2018.	Ph.D., Department of Physics, Graduate School of Science, the University of Tokyo
Oct. 2012.	-	Sep. 2014.	M.S., Department of Physics, Graduate School of Science, the University of Tokyo
Mar. 2002.	-	Aug. 2007.	B.S., Department of Physics, College of Natural Science, Ewha Womans University (Seoul, South Korea)

Work Experiences

Apr. 2024.	-	Present	Assistant Professor / Research Associate Interfaculty Initiative in Information Studies (III) & Graduate School of Interdisciplinary Information Studies , The University of Tokyo
Oct. 2021.	-	Mar. 2024.	Project research associate Laboratory of Computational Genomics , Institute for Quantitative Biosciences (IQB), The University of Tokyo
Apr. 2020.	-	Sep. 2021.	Project researcher Data Science Research Division, Information Technology Center, The University of Tokyo
Nov. 2018.	-	Mar. 2020.	Project researcher Graduate School of Information Science and Technology, The University of Tokyo
Jul. 2007.	-	Jun. 2009.	Research engineer SK hynix (South Korea)

Competitive Research Funding

Sep. 2024.	-	Mar. 2025.	UTOPIA AI Research Discovery Program by AMED	Principal investigator AI-based tool for vesicle transport analysis aimed at elucidating infection routes and drug delivery processes proj. no. 130804PXPX
Oct. 2021.	-	Mar. 2025.	Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))	Co-investigator Dynamic behavior and pathological significance of small RNA in outer membrane vesicles of periodontopathic bacteria proj. no. 21KK0164
Apr. 2020.	-	Mar. 2023.	Grant-in-Aid for Young Scientists	Principal investigator Development of cell image data analysis method for highly accurate 3D vesicle movement detection based on computer vision techniques proj. no. 20K15753
Aug. 2019.	-	Mar. 2021.	Grant-in-Aid for Research Activity start-up	Principal investigator Understanding the intracellular transport of endosomes using machine learning approach proj. no. 19K23717

Academic Honors

Dec. 2024.			Best Paper Award in 17th IEEE NANOMED (International Conference on Nano/Molecular Medicine & Engineering) 2024 • Title: "Image Processing Algorithm for Porphyromonas gingivalis Outer Membrane Vesicle Transport in Periodontal Pathogenesis" [Read Report]
Sep. 2023.			Best Poster Presentation Award in 2023 IIBMP (Informatics in Biology, Medicine and Pharmacology) • Title: "ChromBERT: Identifying Chromatin State Patterns in Human Genome via BERT Techniques"
Oct. 2014.	-	Sep. 2017.	Japanese Government (MEXT) Scholarship for Doctoral Program (Embassy Recommendation)
Apr. 2011.	-	Sep. 2014.	Japanese Government (MEXT) Scholarship for Master's Program (Embassy Recommendation)

Publications

Journal Papers

Luis Augusto Eijy Nagai, Seohyun Lee, and Ryuichiro Nakato: Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform, STAR Protocols, Vol. 5, No. 1:102926, Mar. 2024. [DOI:10.1016/j.xpro.2024.102926]
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: Visualization Method for the Cell-level Vesicle Transport Using Optical Flow and Diverging Colormap, Sensors, Vol. 21(2), No. 522, pp. 1-13, Jan. 2021. [DOI:10.3390/s21020522]
Seohyun Lee, Hyuno Kim, and Hideo Higuchi: Extended Dual-Focus Microscopy for Ratiometric-Based 3D Movement Tracking, Applied Sciences, Vol. 10(18), No. 6243, pp. 1-12, Sep. 2020. [DOI:10.3390/app10186243]
Seohyun Lee and Hideo Higuchi: 3D rotational motion of an endocytic vesicle on a complex microtubule network in a living cell, Biomedical Optics Express, Vol. 10, No. 12, pp. 6611-6624, Nov. 2019. [DOI:10.1364/BOE.10.006611]
Seohyun Lee, Hyuno Kim, and Hideo Higuchi: Numerical method for vesicle movement analysis in a complex cytoskeleton network, Optics Express, Vol. 26, No. 13, pp. 16236-16249, Jun. 2018. [DOI:10.1364/OE.26.016236]

Conference Papers

Seohyun Lee, Hideaki Ota, Hideo Higuchi, Takehiro Yamaguchi, and Ryoma Nakao: Image Processing Algorithm for Porphyromonas gingivalis Outer Membrane Vesicle Transport in Periodontal Pathogenesis, IEEE NANOMED (International Conference on Nano/Molecular Medicine & Engineering) 2024 (Honolulu, United States, 2024. 12) / Proceedings Best Paper Award
Seohyun Lee, Hyuno Kim, and Hideo Higuchi: Automation of detecting and tracking 3D vesicle transport using dual-focus optics, SPIE Photonics West BiOS 2023 (San Francisco, United States, 2023. 2) / Proceedings, 123850E [DOI:10.1117/12.2649474]
Hyuno Kim, Seohyun Lee, and Yuji Yamakawa: Direct face pose estimation using multiple camera views and deep learning, SPIE Photonics West BiOS 2023 (San Francisco, United States, 2023. 2) / Proceedings, 1243814 [DOI:10.1117/12.2651041]
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: Deep learning approach for metastatic cancer cell classification using live-cell imaging data, SPIE Photonics West BiOS 2022 (San Francisco, United States, 2022. 2) / Proceedings, 1196404 [DOI:10.1117/12.2608017] Invited
Seohyun Lee, Hyuno Kim, Hideo Higuchi, Masatoshi Ishikawa, and Nakato Ryuichiro: A Generative Adversarial Network Approach to Metastatic Cancer Cell Images, 2022 IEEE International Conference on Artificial Intelligence in Information and Communication , (Bali, Indonesia, 2022. 2.) as Online conference / Proceedings, pp. 403-406. [DOI:10.1109/ICAIIC54071.2022.9722664]
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: Classification of Metastatic Breast Cancer Cell using Deep Learning Approach, 2021 IEEE International Conference on Artificial Intelligence in Information and Communication , (Jeju island, South Korea, 2021. 4.) as Online conference / Proceedings, pp. 425-428. [DOI:10.1109/ICAIIC51459.2021.9415245]
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: A machine learning approach to transport categorization for vesicle tracking data analysis, SPIE Photonics West BiOS 2021 (San Francisco, United States, 2021. 3) as Online conference / Proceedings, pp. 1-5 [DOI:10.1117/12.2576170]
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: Estimation of Vesicle Transport near the Cellular Membrane using Image Processing, 2020 OSA Imaging and Applied Optics Congress (Vancouver, Canada, 2020. 6.) as Online conference / (JF4E.2)
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: Visualization and Data Analysis for Intracellular Transport using Computer Vision Techniques, 2020 IEEE Sensors Applications Symposium (Kuala Lumpur, Malaysia, 2020. 3.) as Online conference / Proceedings, pp. 1-6 [DOI:10.1109/SAS48726.2020.9220026]
Seohyun Lee, Hyuno Kim, and Masatoshi Ishikawa: Deep Learning Approach to Face Pose Estimation for High-Speed Camera Network System, 2020 IEEE International Conference on Artificial Intelligence in Information and Communication (Fukuoka, Japan, 2020. 2.) / Proceedings, pp. 84-88. [DOI:10.1109/ICAIIC48513.2020.9065051]
Seohyun Lee, Hyuno Kim, Hideo Higuchi, and Masatoshi Ishikawa: Optical flow of vesicles: Computer vision approach for endocytosis of nanoparticles in a living cell, SPIE Photonics West BiOS 2020 (San Francisco, United States, 2020. 2.) / Proceedings, Vol. 11254, pp. 1-6. [DOI:10.1117/12.2543455]
Seohyun Lee, Tomohiko Hayakawa, Chika Nishimura, Satoshi Yawata, Hiroki Yagi, Dai Watanabe, and Masatoshi Ishikawa: Comparison of Deep Learning and Image Processing for Tracking the Cognitive Motion of a Laboratory Mouse, 2019 IEEE Biomedical Circuits and Systems Conference (Nara, Japan, 2019. 10.) / Proceedings, pp. 1-4. [DOI:10.1109/BIOCAS.2019.8919239]
Seohyun Lee, Tomohiko Hayakawa, Chika Nishimura, Satoshi Yawata, Dai Watanabe, and Masatoshi Ishikawa: Movement Analysis for Volitional Direction Change of Laboratory Mouse based on High-Speed Imaging, 2019 OSA Imaging and Applied Optics (Munich, Germany, 2019. 6.) / [DOI:10.1364/ISA.2019.IW1C.1]
Hyuno Kim, Ryo Ito, Seohyun Lee, Yuji Yamakawa, and Masatoshi Ishikawa: Simulation of Face Pose Tracking System using Adaptive Vision Switching, 2019 IEEE Sensors Applications Symposium (Sophia Antipolis, France, 2019. 3.) / Proceedings, pp. 1-6. [DOI:10.1109/SAS.2019.8706000]
Seohyun Lee, Hyuno Kim, Masatoshi Ishikawa, and Hideo Higuchi: 3D Nanoscale Tracking Data Analysis for Intracellular Organelle Movement using Machine Learning Approach, 2019 IEEE International Conference on Artificial Intelligence in Information and Communication (Okinawa, Japan, 2019. 2.) / Proceedings, pp. 181-184 [DOI:10.1109/ICAIIC.2019.8669003]
Seohyun Lee, Hyuno Kim, and Hideo Higuchi: Focus Stabilization by Axial Position Feedback in Biomedical Imaging Microscopy, 2018 IEEE Sensors Applications Symposium (Seoul, South Korea, 2018. 3.) / Proceedings, pp. 309-314. [DOI:10.1109/SAS.2018.8336767]

Presentations

International Meetings

2025	[Poster]	69th Biophysical Society Annual Meeting (Los Angeles, United States)
2024	[Oral]	17th IEEE NANOMED (International Conference on Nano/Molecular Medicine & Engineering) (Honolulu, United States) • Title: "Image Processing Algorithm for Porphyromonas gingivalis Outer Membrane Vesicle Transport in Periodontal Pathogenesis" Best Paper Award
	[Poster]	1st Asia & Pacific Bioinformatics Joint Conference (Okinawa, Japan)
	[Oral]	28th UT-SNU-NCCU International Symposium (Taipei, Taiwan)
2023	[Poster]	2023 SPIE Photonics West BiOS (San Francisco, United States)
2022	[Oral]	4th IEEE International Conference on Artificial Intelligence in Information and Communication (Online)
	[Oral]	2022 SPIE Photonics West BiOS (San Francisco, United States \| Online) Invited
2021	[Oral]	2021 SPIE Photonics West BiOS (San Francisco, United States \| Online)
	[Oral]	3rd IEEE International Conference on Artificial Intelligence in Information and Communication (Online)
2020	[Oral]	IEEE Sensors Applications Symposium (Online)
	[Oral]	2020 OSA Imaging and Applied Optics Congress (Vancouver, Canada \| Online)
	[Poster]	64th Biophysical Society Annual Meeting (San Diego, United States)
	[Poster]	2020 SPIE Photonics West BiOS (San Francisco, United States)
2019	[Poster]	2019 IEEE Biomedical Circuits and Systems Conference (Nara, Japan)
	[Oral]	2019 OSA Imaging and Applied Optics Congress (Munich, Germany)
	[Oral]	1st IEEE International Conference on Artificial Intelligence in Information and Communication (Okinawa, Japan)
2018	[Oral]	IEEE Sensors Applications Symposium (Seoul, South Korea)
2017	[Oral]	9th A3 Foresight Meeting on Biomedicine (Yokohama, Japan)
2013	[Poster]	Joint Workshop on Bio-Soft Matter (Seoul, South Korea)

Domestic Meetings

2025	[Poster]	2nd Joint Symposium on Vaccine Development Hub Projects (Kobe)
	[Oral]	63rd Annual Meeting of the Biophysical Society of Japan [Scheduled] (Nara)
2024	[Oral]	47th Annual Meeting of the Molecular Biology Society of Japan (Fukuoka)
2023	[Poster]	46th Annual Meeting of the Molecular Biology Society of Japan (Kobe)
	[Poster]	12th IIBMP (Informatics in Biology, Medicine and Pharmacology) (Kashiwanoha) • Title: "ChromBERT: Identifying Chromatin State Patterns in Human Genome via BERT Techniques" Best Poster Presentation Award
2022	[Poster]	60th Annual Meeting of the Biophysical Society of Japan (Hakodate)
	[Oral]	11th IIBMP (Informatics in Biology, Medicine and Pharmacology) (Osaka)
	[Oral]	4th Cellular Diversity (Online)
2018	[Oral]	56th Annual Meeting of the Biophysical Society of Japan (Okayama)
	[Oral]	16th Annual Meeting of the Society of Nano Science and Technology (Tokyo)
	[Oral]	Joint meeting on Living Body Movement (Tokyo)
2017	[Oral]	55th Annual Meeting of the Biophysical Society of Japan (Kumamoto)
2016	[Oral]	54th Annual Meeting of the Biophysical Society of Japan (Tsukuba)
2015	[Oral]	53rd Annual Meeting of the Biophysical Society of Japan (Kanazawa)
	[Poster]	13th Annual Meeting of the Society of Nano Science and Technology (Sendai)
	[Oral]	Joint meeting on Living Body Movement (Tokyo)
2014	[Poster]	52nd Annual Meeting of the Biophysical Society of Japan (Sapporo)

Academic Memberships

Apr. 2024	-	Present	Organizing Committee Member, UTokyo-SNU-NCCU International Symposium
Jul. 2022	-	Present	Member, The Molecular Biology Society of Japan
May. 2022	-	Present	Member, Japanese Society for Bioinformatics
Feb. 2021	-	Present	Member, Biophysical Society
Jan. 2021	-	Present	Member, The international Society for Optics and Photonics
Oct. 2019	-	Sep. 2024	Member, Optical Society of America
Jul. 2014	-	Present	Member, The Biophysical Society of Japan

Academic and Educational Activities

Sep. 2025			[Scheduled to] Organize Mini-Symposium at the 63rd Annual Meeting of the Biophysical Society of Japan: "Unlocking Vesicle Dynamics: Advanced Imaging, AI, and Biomedical Applications" (Co-organizer: Prof. Higuchi)
Mar. 2025			Tutor at KI-UT Course: Bioinformatics Analysis and Visualisation of Medical Genomics Data (Karolinska Institutet – The University of Tokyo collaborative course)
Jun. 2021			TESOL Certification from Arizona State University
Feb. 2013	-	Aug. 2013	English teacher at Association for Promotion of International Understanding
Jul. 2005	-	Jul. 2006	Exchange student in Technische Universität Darmstadt (Darmstadt, Germany)

Additional Information

Languages: Korean (Native), English (Fluent), Japanese (Fluent), German (Elementary), Chinese (Beginner)
Interests: Reading books, crocheting, practicing yoga, and listening to Taylor Swift (Hi there, Swifties! )